Neotoma genomics

We are interested in studying the genetic nature of adaptation in spatially heterogeneous environments in N. fuscipes. The Dusky-footed woodrat is an ideal candidate for such an investigation, due to its wide geographic distribution that includes many different habitat and climatic conditions. Additionally, other species within Neotoma have shown strong responses to temperature change through time (Smith and Betancourt 1998, Smith et al. 2014). Postdoc Sarah Brown is spearheading a project in the lab where we use a next generation sequencing approach (complete mitogenomes and ddRAD seq) in both modern and ancient samples to 1) elucidate changes in demography through time and in relation to past climate change, and 2) identify genetic loci that might be linked to environmental adaptation in modern samples, and then screen ancient individuals for similar signatures of adaptation. Our ultimate goal is to identify loci that show adaptation to climatic/environmental conditions in modern N. fuscipes, and then screen ancient samples for similar patterns.

Targeted samples of modern Neotoma fuscipes individuals across California

Modern woodrat tissues from the UC MVZ awaiting extraction

Our good luck PCR tchotchkes. Gotta rub then for the PCRs to work. Seriously.